I have found that .1 layer height is not always best. When printing D&D miniatures using the .25 nozzle I found .14 worked better. The .1 took a lot longer and seemed as if it over heated the part due to the many passes. And it seemed to me a such a slow flow rate that the plastic would cook in the nozzle waiting to be extruded also causing flow issues.(PLA) The cooked thing is just something I imagine could happen, never read anything about that nor would it cause your issue.
There is also an issue of the glass plate moving and causing issues.. not sure if you already addressed that in a previous thread.. was only a couple of weeks ago this came up. Shimming the corner between the plate and rubber block is how I dealt with it.
Make sure the model passed the manifold and intersecting surfaces tests under Repair. I have read more than a few posts on S3D forum where things don't print correctly with S3D but do with Cura and most often there are errors in the model Cura ignores but S3D does not and it causes issues.
Hope something I babbles help you find the cause.

Airscapes, I appreciate your babbles! I do often over look the most simplest of things....

Yes, I seem to have more issues when printing 0.1mm layer height. The person I am printing these for has requested that layer height and I can't really change things now. If they need further parts I will be trying to convince them 0.15 would be adequate, but I know he is particular about the final surface finish of the parts, and why I'm most concerned. But, yes. 0.1mm is painfully slow.

I have had the glass plate slip on me a few times and learnt early on after getting my M3 that those clips need to be tight. I need to get around printing those adjustable glass bed mounts.

Model did pass the manifold test. I am fairly familiar with polygon modelling having worked in the 3D graphics industry for the past 20 years. I checked the part in my modelling program before importing into S3D.

For now I'm going with Cura. I have a decent enough profile setup after messing with it all day today. I think the results are a lot nicer.

The other issue, or probably the same - see attached. The surfaces on the side of the model are being sucked in around the screw holes, or so it seems. It's a lot more noticeable on the S3D print, as well as the less then vertical walls. Could it be an infill setting? I'm using lines at 30%. 5 bottom layers and 6 top layers. With Cura it seems a lot less severe. My other printer (prusa i3 mk3) and sliced in Slic3r, same filament and the surface is close to perfect. It's a strange one for me.... can't seem to work it out.

Thanks again airscapes. The STL I can't share as it belongs to a company. The filament in these pics is eSun ABS+ and I have also tried Zortrax ABS with same results. The Zortrax ABS prints at a much higher temp of 270, the eSun at 240.

I printed the whole part last night using the Cura sliced gcode and it turned out very similar to the S3D print, possibly slightly better. So, slicing off a portion of the model to use as a test is not a fair comparison in this case.

I will take some print screen images of my S3D settings today and post. Hopefully somebody will see straight away what I'm doing wrong

Good to hear it!
Another thing I did with layer height with the miniatures and not sure it is even valid really.. but I would find the max height of the model and choose the layer height that would divide most evenly into it (above .1 and below .2)